Bis(terpyridine)-based surface template structures on graphite: a force field and DFT study

Patterned graphene: An effective platform for adsorption, immobilization, and destruction of SARS-CoV-2 Mpro

To address the ongoing challenges posed by the SARS-CoV-2 and potentially stronger viruses in the future, the development of effective methods to fabricate patterned graphene (PG) and other precisely functional products has become a new research frontier. Herein, we modeled the "checkerboard" graphene (CG) and stripped graphene (SG) as representatives of PG, and studied their interaction mechanism with the target protein (Mpro) by molecular dynamics simulation. The calculation results on the binding strength and the root mean square deviation values of the active pocket revealed that PG is an effective platform for adsorption, immobilization, and destruction of Mpro. Specifically, CG is found to promote disruption of the active pocket for Mpro, but the presence of "checkerboard" oxidized regions inhibits the adsorption of Mpro. Meanwhile, the SG can effectively confine Mpro within the non-oxidized strips and enhances their binding strength, but doesn't play well on disrupting the active pocket. Our work not only elucidates the biological effects of PGs, but also provides guidance for their targeted and precise utilization in combating the SARS-CoV-2.

Turning the structure of the Aβ42 peptide by different functionalized carbon nanotubes: a molecular dynamics simulation study

Functionalized carbon nanotubes (CNTs) can inhibit the self-assembly of amyloid-beta (Aβ) peptides. Under abnormal conditions, the structure of the Aβ peptides undergoes a fundamental transformation, and this transformation will induce conformational conversions of other polymerized Aβ peptides. Here, we explore the interactions between different functionalized CNTs and Aβ₄₂ peptides by molecular dynamics simulations. Our results show that compared to the original CNTs, the highly functionalized CNTs induce different adsorption patterns of the peptides. This adsorption pattern destroys the α-helix structure and increases the β-turn and random coil content significantly. The hydrogen bonds formed by the peptide and water molecules or CNTs further reveal the reasons for the structural transformation of the peptide. Due to electrostatic interactions and π-π stacking interactions, some amino acids (such as Phe4, Lys16, Phe20, and Lys28) are tightly fixed on the surfaces, and other amino acids move around these amino acids to accelerate the unfolding and denaturation of the peptide. Our research shows that functionalized CNTs have excellent potential to inhibit the abnormal aggregation of Aβ₄₂ peptides. Our research also provides theoretical guidance in the design and synthesis of carbon nanomedicines for protein conformation diseases.

The Inhibition of SARS-CoV-2 3CL Mpro by Graphene and Its Derivatives from Molecular Dynamics Simulations

At present, the most powerful new drugs for COVID-19 are antibody proteins. In addition, there are some star small molecule drugs. However, there are few studies on nanomaterials. Here, we study the intact graphene (IG), defective graphene (DG), and graphene oxide (GO) interacting with COVID-19 protein. We find that they show progressive inhibition of COVID-19 protein. By using molecular dynamics simulations, we study the interactions between SARS-CoV-2 3CL Mpro and graphene-related materials (GRMs): IG, DG, and GO. The results show that Mpro can be absorbed onto the surfaces of investigated materials. DG and GO interacted with Mpro more intensely, causing the decisive part of Mpro to become more flexible. Further analysis shows that compared to IG and GO, DG can inactivate Mpro and inhibit its expression effectively by destroying the active pocket of Mpro. Our work not only provides detailed and reliable theoretical guidance for the application of GRMs in treating with SARS-CoV-2 but also helps in developing new graphene-based anti-COVID-19 materials.

Modeling of low temperature adsorption of hydrogen in carbon nanopores

We simulated the low temperature (T = 77 K) hydrogen adsorption in carbon slit-shaped nanopores using consecutively united atom (UA) and all atom (AA) representation of hydrogen molecule. We showed that both approximations give comparable estimation of the amount stored, for the wide range of pore width (0.6-2.5 nm). We also showed that at very high pressure (P = 400 bar, corresponding to the fugacity f used in grand canonical Monte Carlo simulations of f = 800 bar) the density of the adsorbed hydrogen structures is larger than the density of bulk liquid at critical temperature (∼76 kg/m³). This result agrees with the experimental observation of the density of the order of 100 kg/m³ for the hydrogen adsorbed in microporous carbons, reported recently in the literature.

Novel scroll peapod produced by spontaneous scrolling of graphene onto fullerene string

Novel scroll peapods are fabricated simply by utilizing the spontaneous scrolling mechanism of graphene onto fullerene string.

Free-Standing Monolayer Two-Dimensional Supramolecular Organic Framework with Good Internal Order

Utilizing dynamic self-assembly and self-sorting to obtain large-area, molecularly precise monolayered structures represents a promising approach toward two-dimensional supramolecular organic frameworks (2D SOF) or 2D supramolecular polymers. So far, related approaches suffer from small domain sizes, fragility and weak long-range internal order. Here we report on the self-assembly of a host-guest enhanced donor-acceptor interaction, consisting of a tris(methoxynaphthyl)-substituted truxene spacer, and a naphthalene diimide substituted with N-methyl viologenyl moieties as donor and acceptor monomers, respectively, in combination with cucurbit[8]uril as host monomer toward monolayers of an unprecedented 2D SOF. Featuring orthogonal solubility, the participating molecules self-assemble at a liquid-liquid interface, yielding exceptionally large-area, insoluble films, which were analyzed by transmission electron microscopy, atomic force microscopy and optical microscopy to be monolayers with a thickness of 1.8 nm, homogeneously covering areas up to 0.25 cm(2), and featuring the ability to be free-standing over holes of 10 μm(2). Characterization with ultraviolet-visible absorption spectroscopy, solid-state nuclear magnetic resonance spectroscopy, infrared spectroscopy, and grazing incidence wide-angle X-ray scattering allowed for confirmation of a successful complexation of all three monomers toward an internal long-range order and gave indications to an expected hexagonal superstructure. Our results extend the existing variety of two-dimensional soft nanomaterials by a versatile supramolecular approach, whereas the possibility of varying the functional monomers is supposed to open adaptability to different applications like membranes, sensors, molecular sieves, and optoelectronics.

Mechanism of graphene oxide as an enzyme inhibitor from molecular dynamics simulations

Graphene and its water-soluble derivative, graphene oxide (GO), have attracted huge attention because of their interesting physical and chemical properties, and they have shown wide applications in various fields including biotechnology and biomedicine. Recently, GO has been shown to be the most efficient inhibitor for α-chymotrypsin (ChT) compared with all other artificial inhibitors. However, how GO interacts with bioactive proteins and its potential in enzyme engineering have been rarely explored. In this study, we investigate the interactions between ChT and graphene/GO by using molecular dynamics (MD) simulation. We find that ChT is adsorbed onto the surface of GO or graphene during 100 ns MD simulations. The α-helix of ChT plays as an important anchor to interact with GO. The cationic and hydrophobic residues of ChT form strong interactions with GO, which leads to the deformation of the active site of ChT and the inhibition of ChT. In comparison, the active site of ChT is only slightly affected after ChT adsorbed onto the graphene surface. In addition, the secondary structure of ChT is not affected after it is adsorbed onto GO or graphene surface. Our results illustrate the mechanism of the interaction between GO/graphene and enzyme and provide guidelines for designing efficient artificial inhibitors.

Nature of the attractive interaction between proton acceptors and organic ring systems

Systematic ab initio calculations are combined with a deconvolution of electrostatic contributions to analyze the interplay between potential hydrogen bond acceptors and organic rings with C(sp(2))-H groups (benzene, pyridine and cyclopentadiene). A distinct anisotropic interaction between the ring systems and the electron lone pairs of cyanide, water and other acceptor species is revealed that favors the in-plane orientation of the proton acceptor group. In the attractive regime this interaction carries a pronounced electrostatic signature. By decomposing the electrostatic contribution into parts attributed to different subunits of the ring systems we demonstrate that a major proportion of the interaction energy gain is originating from the non-adjacent moieties, that are not in close contact with. This behavior holds equally for homocyclic, heterocyclic and non-aromatic rings but contrasts that of the ethyne molecule, taken as reference for a weak hydrogen bond donor clearly exhibiting the expected localized character. The ring interaction requires the presence of π-electron clouds and typically results in an interaction energy gain of 40 to 80 meV. Our findings suggest the proton acceptor-ring interaction as a new category of intermolecular non-covalent interactions.

Influence of the solvent on the stability of bis(terpyridine) structures on graphite

The effect of solvation on the adsorption of organic molecules on graphite at room temperature has been addressed with force-field molecular dynamics simulations. As a model system, the solvation of a bis(terpyridine) isomer in water and 1,2,4-trichlorobenzene was studied with an explicit solvation model. The inclusion of solvation has a noticeable effect on adsorption energies. Although the results of the various considered force fields differ quite significantly, they all agree that the adsorption of BTP from the TCB solvent is almost thermoneutral. The substrate simply acts as a template to allow a planar arrangement of the network, which is stabilized by the intermolecular interaction. Using an atomic thermodynamics approach, the order of the stability of various network structures as a function of the chemical potential is derived yielding a sequence in agreement with the experiment.

Structural and electronic properties of oligo- and polythiophenes modified by substituents

The electronic and structural properties of oligo- and polythiophenes that can be used as building blocks for molecular electronic devices have been studied by using periodic density functional theory calculations. We have in particular focused on the effect of substituents on the electronic structure of thiophenes. Whereas singly bonded substituents, such as methyl, amino or nitro groups, change the electronic properties of thiophene monomers and dimers, they hardly influence the band gap of polythiophene. In contrast, phenyl-substituted polythiophenes as well as vinyl-bridged polythiophene derivatives exhibit drastically modified band gaps. These effects cannot be explained by simple electron removal or addition, as calculations for charged polythiophenes demonstrate.

Septipyridines as conformationally controlled substitutes for inaccessible bis(terpyridine)-derived oligopyridines in two-dimensional self-assembly

The position of the peripheral nitrogen atoms in bis(terpyridine)-derived oligopyridines (BTPs) has a strong impact on their self-assembly behavior at the liquid/HOPG (highly oriented pyrolytic graphite) interface. The intermolecular hydrogen bonding interactions in these peripheral pyridine units show specific 2D structures for each BTP isomer. From nine possible constitutional isomers only four have been described in the literature. The synthesis and self-assembling behavior of an additional isomer is presented here, but the remaining four members of the series are synthetically inaccessible. The self-assembling properties of three of the missing four BTP isomers can be mimicked by making use of the energetically preferred N-C-C-N transoid conformation between 2,2'-bipyridine subunits in a new class of so-called septipyridines. The structures are investigated by scanning tunneling microscopy (STM) and a combination of force-field and first-principles electronic structure calculations.

Intermolecular vs molecule-substrate interactions: A combined STM and theoretical study of supramolecular phases on graphene/Ru(0001)

The competition between intermolecular interactions and long-range lateral variations in the substrate-adsorbate interaction was studied by scanning tunnelling microscopy (STM) and force field based calculations, by comparing the phase formation of (sub-) monolayers of the organic molecules (i) 2-phenyl-4,6-bis(6-(pyridin-3-yl)-4-(pyridin-3-yl)pyridin-2-yl)pyrimidine (3,3'-BTP) and (ii) 3,4,9,10-perylene tetracarboxylic-dianhydride (PTCDA) on graphene/Ru(0001). For PTCDA adsorption, a 2D adlayer phase was formed, which extended over large areas, while for 3,3'-BTP adsorption linear or ring like structures were formed, which exclusively populated the areas between the maxima of the moiré structure of the buckled graphene layer. The consequences for the competing intermolecular interactions and corrugation in the adsorption potential are discussed and compared with the theoretical results.

Two-dimensional molecular organization of pyridinecarboxylic acids adsorbed on graphite

Pyridinecarboxylic acids 3-9 are adsorbed from solution onto graphite to produce well-ordered adlayers that can be imaged by scanning tunneling microscopy. Hydrogen bonds involving the carboxyl groups and the nitrogen atom of the pyridyl ring play key roles in controlling the observed two-dimensional (2D) organization. Pyridinecarboxylic acids have a strong tendency to associate to form hydrogen-bonded chains and cyclic oligomers, which then pack to produce sheets. The preference for sheets ensures that molecular organization in 2D and 3D typically shows a significant degree of homology. Together, our observations highlight the potential of engineering similarly ordered 2D and 3D structures built from simple compounds that combine an inherent affinity for surfaces with an ability to engage in strong coplanar intermolecular interactions.